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. Author manuscript; available in PMC: 2012 Feb 15.
Published in final edited form as: Biochemistry. 2011 Jan 24;50(6):962–969. doi: 10.1021/bi101724h

Table 2.

Thermodynamic stability of duplex formation of RNAs with and without AC mismatches at pH 7.0 or pH 5.5.

Duplexes with Loops
Average of Two-State Melt Curve Fits
 Linear Fit to 1/TM vs ln(CT/4) Plots
−ΔH0
(kcal/mol)		 −ΔS0
(cal/K•mol)		 −ΔG037
(kcal/mol)		 −TM
(0C)		 −ΔH0
(kcal/mol)		 −ΔS0
(cal/K•mol)		 −ΔG037
(kcal/mol)		 −TM
(0C)		 ΔGo37, loop
(kcal/mol)		 ΔΔGpH
(kcal/mol)
CA IL12 5′-CCGAAGCCG-3′
3′-GGCUCUGGC-5′		 86.47±10.95 251.39±35.08 8.50±0.08 44.2 99.48±5.69 292.90±18.09 8.63±0.09 43.7 1.57±0.35 0.86
90.75±9.27 262.23±29.29 9.42±0.20 47.2 95.23±3.61 276.44±11.35 9.49±0.09 47.0
CA IL14 5′-CCGGAGCCG-3′
3′-GGCUCUGGC-5′		 79.23±8.40 227.69±26.24 8.61±0.128 45.4 79.22±0.94 227.70±2.98 8.60±0.02 45.3 2.50±0.96 0.14
67.62±11.75 191.30±37.51 8.29±0.17 45.3 75.87±7.40 217.35±23.41 8.46±0.22 45.1
CA IL15 5′-CCGUAUCCG-3′
3′-GGCGCGGGC-5′		 74.33±29.18 217.14±94.63 6.99±0.33 38.9 109.47±3.35 331.05±10.86 6.79±0.02 37.7 4.35±0.97 0.28
57.84±14.51 164.18±47.52 6.92±0.40 39.1 119.90±4.21 365.57±13.66 6.51±0.035 37.0
CA IL19 5′-CCGAAGCCG-3′
3′-GGCUCCGGC-5′		 83.08±13.72 231.99±41.95 11.13±0.72 55.2 79.85±5.27 222.11±16.16 10.97±0.27 55.2 2.23±0.31 2.26
90.24±12.15 250.78±36.94 12.46±0.70 58.8 103.27±3.45 290.32±10.47 13.23±0.20 58.5
CA IL20 5′-CCGGAGCCG-3′
3′-GGCUCCGGC-5′		 82.50±21.80 231.10±66.92 10.82±1.01 54.0 65.69±1.55 179.24±4.77 10.09±0.07 54.8 2.80±0.31 1.80
82.38±17.92 228.84±54.69 11.40±0.958 56.5 91.52±6.72 256.73±20.53 11.89±0.37 56.3
CA IL21 5′-CCGGACCCG-3′
3′-GGCUCGGGC-5′		 87.21±14.16 142.12±43.51 12.12±0.87 58.2 89.14±3.15 248.01±9.58 12.22±0.18 58.1 0.78±0.32 0.87
93.05±11.44 264.20±34.55 13.11±0.72 60.1 94.92±1.76 263.84±5.31 13.09±0.11 60.0
CA IL23 5′-CCGCAACCG-3′
3′-GGCGCUGGC-5′		 99.35±12.45 283.05±38.39 11.56±0.55 53.6 119.34±2.47 344.72±7.93 12.43±0.11 53.1 2.28±0.21 0.39
81.95±11.80 227.58±35.95 11.36±0.65 56.4 95.40±1.65 268.76±5.05 12.04±0.08 53.6
CA IL27 5′-CCGCACCCG-3′
3′-GGCGCGGGC-5′		 75.71±7.75 203.58±23.23 12.57±0.53 63.9 79.10±1.69 213.67±5.08 12.83±0.12 63.8 0.79±0.29 2.01
116.26±18.0 320.74±53.22 16.78±1.47 67.0 93.10±2.05 252.34±6.06 14.84±0.16 67.4
Duplexes without Loops
Average of Two-State Melt Curve Fits
 Linear Fit to 1/TM vs ln(CT/4) Plots
−ΔH0
(kcal/mol)		 −ΔS0
(cal/K•mol)		 −ΔG037
(kcal/mol)		 −TM
(0C)		 −ΔH0
(kcal/mol)		 −ΔS0
(cal/K•mol)		 −ΔG037
(kcal/mol)		 −TM
(0C)
5′-CCGCCG-3′
3′-GGCGGC-5′		 57.52±8.88 152.79±27.01 10.13±0.51 57.7 56.84±1.13 150.53±4.46 10.15±0.06 58.1
58.44±10.67 155.43±32.62 10.23±0.57 58.0 53.38±1.18 139.75±3.62 10.04±0.06 58.8
Duplex
12		 5′-CCGAGCCG-3′
3′-GGCUUGGC-5′		 80.12±5.31 223.72±16.37 10.73±0.23 54.2 80.42±2.42 224.64±7.44 10.75±0.11 54.2
Duplex
14		 5′-CCGGGCCG-3′
3′-GGCUUGGC-5′		 71.76±1.81 199.3±5.73 9.84±0.18 52.0 92.42±2.20 263.70±6.83 10.63±0.08 51.4
Duplex
15		 5′-CCGUUCCG-3′
3′-GGCGGGGC-5′		 110.48±9.29 320.39±29.02 11.11±0.31 50.4 98.18±3.89 282.15±12.07 10.67±0.14 50.6
Duplex
19		 5′-CCGAGCCG-3′
3′-GGCUCGGC-5′		 91.02±6.25 247.13±18.41 14.38±0.54 66.3 102.31±1.86 280.58±5.50 15.28±0.15 66.0
Duplex
20		 5′-CCGGGCCG-3′
3′-GGCUCGGC-5′		 98.78±3.88 271.44±11.64 14.59±0.27 64.6 104.45±2.29 288.38±6.84 15.00±0.17 64.4
Duplex
21		 5′-CCGGCCCG-3′
3′-GGCUGGGC-5′		 95.85±8.87 262.87±26.38 14.32±0.67 64.4 111.31±0.89 308.88±2.65 15.51±0.07 64.2
Duplex
23		 5′-CCGCACCG-3′
3′-GGCGUGGC-5′		 114.69±2.51 316±7.42 16.42±0.21 66.3 119.47±2.07 330.96±6.14 16.82±0.17 66.2
Duplex
27		 5′-CCGCCCCG-3′
3′-GGCGGGGC-5′		 91.56±6.41 241.02±18.78 16.81±0.58 76.2 92.39±2.84 243.45±8.33 16.88±0.25 76.1